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Identification of Genetic Variants in CFAP221 As a Cause of Primary Ciliary Dyskinesia

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Identification of Genetic Variants in CFAP221 As a Cause of Primary Ciliary Dyskinesia HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author J Hum Genet Manuscript Author . Author manuscript; Manuscript Author available in PMC 2020 April 21. Published in final edited form as: J Hum Genet. 2020 January ; 65(2): 175–180. doi:10.1038/s10038-019-0686-1. Identification of Genetic Variants in CFAP221 as a Cause of Primary Ciliary Dyskinesia Ximena M. Bustamante-Marin1,#, Adam Shapiro2,#, Patrick R. Sears1, Wu-Lin Charng3, Donald F. Conrad3,4, Margaret W. Leigh5, Michael R. Knowles1, Lawrence E. Ostrowski1,*, Maimoona A. Zariwala6,* 1Department of Medicine, Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina., NC 27599, USA. 2Department of Pediatrics, Division of Pediatric Respiratory Medicine, McGill University Health Centre Research Institute, Montreal, Quebec. 3Department of Genetics and Psychiatry, Washington University School of Medicine, St. Louis, MO 63110, USA 4Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, 97006, USA 5Department of Pediatrics, Marsico Lung Institute, University of North Carolina, Chapel Hill, North Carolina, 27599. 6Department of Pathology and Laboratory Medicine, Marsico Lung Institute University of North Carolina, Chapel Hill, NC 27599, USA. Abstract Users may view, print, copy, and download text and data-mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use:http://www.nature.com/authors/editorial_policies/license.html#terms * Corresponding Author: Lawrence E. Ostrowski, 104 Manning Dr Room 6021, [email protected], Phone: 919-8437177, Maimoona A. Zariwala, 7219 A Marsico Hall, [email protected], Phone: 919-966-7050, Fax: 919-966-5178. #Ximena M. Bustamante-Marin and Adam Shapiro are co-first authors. *Lawrence E. Ostrowski and Maimoona A. Zariwala contributed equally to this research. Contributors: XBM and LEO wrote the manuscript and MRK and MAZ contributed to the manuscript. XBM, MRK, MAZ and LEO conceived the experiments, and designed strategies. XBM cultured the HNE cells, and performed experiments, and MAZ performed genotyping and segregation analysis. XBM, LEO, PS, and MAZ analyzed and interpreted data. AS, MWL, MAZ and MRK, identified the patient and performed exome sequencing. DFC and WC performed the whole exome sequencing analysis, AS performed nasal scrape, and PS, performed waveform analysis. All authors reviewed the manuscript. Patient consent: Obtained. Ethics approval: Provenance and peer review not commissioned; externally peer reviewed. Web resources: PSAP, https://github.com/awilfert/PSAP-pipeline OMIM, http://www.omim.org GenBank, https://www.ncbi.nlm.nih.gov/genbank/ Ensembl, http://grch37.ensembl.org/Homo_sapiens/Info/Index 1000Genome, http://www.internationalgenome.org/ gnomAD, http://gnomad.broadinstitute.org/ Uniprot, https://www.uniprot.org/ dbSNP, https://www.ncbi.nlm.nih.gov/snp Supplementary information is available at the Journal of Human Genetics’ website. Conflict of interest The authors declare no conflicts of interest Bustamante-Marin et al. Page 2 Primary ciliary dyskinesia (PCD) is a rare disorder that affects the biogenesis or function of motile Author ManuscriptAuthor Manuscript Author Manuscript Author Manuscript Author cilia resulting in chronic airway disease. PCD is genetically and phenotypically heterogeneous, with causative mutations identified in over 40 genes; however, the genetic basis of many cases is unknown. Using whole exome sequencing, we identified three affected siblings with clinical symptoms of PCD but normal ciliary structure, carrying compound heterozygous loss-of-function variants in CFAP221. Computational analysis suggests that these variants are the most damaging alleles shared by all three siblings. Nasal epithelial cells from one of the subjects demonstrated slightly reduced beat frequency (16.5 Hz vs 17.7 Hz, p=0.16); however, waveform analysis revealed that the CFAP221 defective cilia beat in an aberrant circular pattern. These results show that genetic variants in CFAP221 cause PCD and that CFAP221 should be considered a candidate gene in cases where PCD is suspected but cilia structure and beat frequency appear normal. Keywords Primary ciliary dyskinesia; PCD; CFAP221; PCDP1; ciliary waveform Introduction Primary ciliary dyskinesia (PCD) is a rare genetic disease (MIM: 244400), caused by genetic lesions that impair the function of the motile cilia that line the airways, thereby reducing mucociliary clearance and resulting in chronic respiratory infections. Currently there are no specific treatments available for PCD, and early diagnosis is crucial to ensure proper disease management and minimize loss of lung function1. Advances in whole exome sequencing and analysis have contributed to the identification of PCD-causing mutations in >40 genes2. However, the underlying genetic cause is still unknown in ~30% of PCD cases, and in subjects with no obvious defects in ciliary structure or beat frequency, establishing a firm diagnosis remains challenging. Material and Methods Subjects Individuals included in the study had a clinical diagnosis of PCD confirmed by standard clinical diagnostic criteria. For studies of affected individuals and their families, a signed and informed consent was obtained from all participants. All protocols involving human studies were approved by University of North Carolina Medical School and/or McGill University Health Centre Research Institute Institutional Review Boards. Genetic Analysis Identification of CFAP221 variants was performed by whole exome sequence analysis using the population sampling probability (PSAP) framework as previously described3, as detailed in Supplementary Information. J Hum Genet. Author manuscript; available in PMC 2020 April 21. Bustamante-Marin et al. Page 3 Airway epithelial cell cultures Author ManuscriptAuthor Manuscript Author Manuscript Author Manuscript Author Human nasal epithelial (HNE) cells from proband 2-I and controls were obtained as previously described4. The nasal cells were expanded as conditionally reprogrammed cells (CRC)5 and cultured as previously described6. Human bronchial epithelial (HBE) cells were cultured at the air/liquid interphase (ALI) as previously described7. These protocols have been approved by the University of North Carolina (UNC) Medical School Institutional Review Board. Reverse transcription polymerase chain reaction (RT-PCR) Semi-quantitative RT-PCR was performed using standard protocols (Takara Bio USA, Inc.), as detailed in Supplementary Information. Waveform analysis and ciliary beat frequency measurements To evaluate the waveform and beat direction, high resolution videos of ciliated cells were recorded and analyzed as described in Supplementary Information. Results and Discussion We identified three French-Canadian siblings from family UNC-1200 (Figure 1A) with phenotypes suggestive of PCD (Supplementary Table 1), including neonatal respiratory distress, chronic sinus disease, recurrent otitis media, and bronchiectasis in two individuals. None of the subjects had situs inversus. Sweat chloride testing and immunology investigations were normal in all three siblings. The rate of nasal nitric oxide production (nNO) was normal (122, 171, 189 nL/min; cut-off of 77 nL/min8), and examination of ciliary axonemes by TEM did not reveal obvious ultrastructural defects (Figure 1B). We carried out whole exome sequencing in one proband (2-II) and analyzed the resulting genotype data using a statistical framework for assessing the significance of variants from n=1 cases of rare genetic disease3. This identified compound heterozygous variants in cilia and flagella associated protein 221 (CFAP221; [GenBank: NM_001271049.2, Chr.2q14.2] previously known as PCDP1) as the most damaging variants in the genome of 2-II and most plausible cause of a rare recessive disorder (Table 19, 10 and Figure 1C). Segregation analysis confirmed that both variants were present in all three affected siblings and parents were carriers for each variant (Supplementary Figure 1). A frameshift variant in exon 22 [c. 2303_2307delTAGAA p.Leu768HisFs*5] is predicted to result in a premature termination codon. The other variant (c.2318+1G>A) disrupts a canonical splice donor site in intron 22 that causes aberrant splicing (Figure 1C)9. RT-PCR analysis of exon 22, using primers spanning exon 19–23, of control human nasal epithelial (HNE) cells amplified a 539 base pair product (Figure 1C). In HNE cells from subject 2-I we confirmed the five base pair deletion (r.2303_2307del) resulting in a premature stop codon (Figure 1C). Analysis of the intron 22 splice site variant revealed the in frame deletion of exon 22 (r.2226_2318del).This is predicted to result in deletion of 31 amino acid residues (p.Cys743_Arg773del) (Figure 1C). J Hum Genet. Author manuscript; available in PMC 2020 April 21. Bustamante-Marin et al. Page 4 We examined the expression and localization of CFAP221 in normal human bronchial Author ManuscriptAuthor Manuscript Author Manuscript Author Manuscript Author epithelial (HBE) cells (Supplementary Figure 2) cultured at an air/liquid interface (ALI)7. RT-PCR demonstrated that the expression of CFAP221 increased during ciliated cell differentiation (Supplementary Figure 2A). Western blotting and immunofluorescence showed that CFAP221 is not expressed in undifferentiated airway cells, and is localized primarily to the axoneme in differentiated ciliated cells (Supplementary Figure 2B and 2C). To investigate
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